The approval of Adani's Carmichael coal mine in central Queensland has been set aside by the Federal Court because of a bureaucratic bungle over two vulnerable species.

The $16 billion open cut and underground coal mine and 189-kilometre rail link was approved by the Federal Government in July 2014.

The approval was set aside by the court after it was found Federal Environment Minister Greg Hunt had not properly considered advice about the yakka skink and the ornamental snake.

The Mackay Conservation Group launched a challenge to the mine project earlier this year over the vulnerable species.

Today's court ruling has been consented to by Indian company Adani and the Federal Government.

Mr Hunt denied it was a major problem.

"What the department said is 'look, we have a sense that the court might find something new as a new standard and so it might be better to remake the decision'," he said.

In a statement, the Federal Department of the Environment said the ruling was taken at the request of "all of the parties to the court proceedings".

It said the entire approval process would not have to be reconsidered.

"This is a technical, administrative matter and to remove this doubt, the department has advised that the decision should be reconsidered," the statement said.

Legal loopholes are paving the way for anti-coal activists to delay billions of dollars in investment and thousands of jobs in Queensland.

Qld Resources Council CEO Michael Roche

"Without pre-empting a final decision about the project, the department expects that it will take six to eight weeks to prepare its advice and the supporting documentation, and for the Minister to reconsider his final decision."

Environmental Defenders Office principal solicitor Sue Higginson, who represents the Mackay Conservation Group, said the coal mine, which would be the biggest in Australia, was now in a state of legal uncertainty.

She has written to Mr Hunt with further information to consider for the mine's application, namely "exaggerated" job figures included in Adani's environmental impact statement.

"What can happen from here is the Minister can re-make his decision, and of course in re-making that decision he can approve the mine again following the proper legal procedures, or he can refuse the mine; that is the legal power open to the Minister," Ms Higginson said.

"What our client says is that if the Minster wants to reconsider approving the mine there is a plethora of new evidence and information about that mine, so it will be no simple task to simply re-approve that mine."

Adani said it was committed to ensuring its mine, rail and port projects in Queensland are developed, and complied with environmental conditions.

"It should be noted the approval did include appropriate conditions to manage the species protection of the yakka skink and ornamental snake," it said.

"However, we have been advised that, because certain documents were not presented by the Department in finalising the approval, it created a technical legal vulnerability that is better to address now.

"Adani is confident the conditions imposed on the existing approval are robust and appropriate once the technicality is addressed."

Queensland Resources Council chief executive Michael Roche said "legal loopholes" had paved the way for anti-coal activists to delay billions of dollars in investment and thousands of jobs.

"It is preposterous that a technical administrative hitch could hold up billions of dollars in investment and thousands of desperately needed jobs," Mr Roche said.

Mr Roche said Mr Hunt should be able to quickly sort it out.

"The great irony of this is that minister has put conditions in his approval for the mine that cover the two species - a skink and a snake - but on some technical basis he can't demonstrate that all the right documents were in front of him at the time," he said.

State Mines Minister Anthony Lynham said he hoped the court's decision would not delay the project for too long.

"I'm extremely disappointed this has happened," he said.

"There's been a judicial review and I believe it's a technical error, but we're asking the Federal Government, we're asking the Federal Environment Minister to sort this out as quickly as possible."

However, Greens senator Larissa Waters said Adani should now walk away from Carmichael mine in the wake of the Federal Court decision.

"This is a chance now for Adani to walk away and if they do seek a fresh approval from the Minister, Minister Hunt needs to not only consider the conservation advices he forgot about the first time but he also needs to consider the fact that Adani corrected the record about the claims they made about jobs," she said.

You have no doubt been hearing a lot about the Paris Agreement and know that it pertains to climate change, but are too embarrassed at this stage to ask for an overall explanation of what it's all about.